A virtual alternative to molecular model sets: a beginners' guide to constructing and visualizing molecules in open-source molecular graphics software.
Ontology highlight
ABSTRACT: Objective
The application of molecular graphics software as a simple and free alternative to molecular model sets for introductory-level chemistry learners is presented.Results
Based on either Avogadro or IQmol, we proposed four sets of tasks for students, building basic molecular geometries, visualizing orbitals and densities, predicting polarity of molecules and matching 3D structures with bond-line structures. These topics are typically covered in general chemistry for first-year undergraduate students. Detailed step-by-step procedures are provided for all tasks for both programs so that instructors and students can adopt one of the two programs in their teaching and learning as an alternative to molecular model sets.
SUBMITTER: Phankingthongkum S
PROVIDER: S-EPMC7887714 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:We present an open-source, interactive program named Proteoform Suite that uses proteoform mass and intensity measurements from complex biological samples to identify and quantify proteoforms. It constructs families of proteoforms derived from the same gene, assesses proteoform function using gene ontology (GO) analysis, and enables visualization of quantified proteoform families and their changes. It is applied here to reveal systemic proteoform variations in the yeast response to salt stress.
| S-EPMC5770237 | biostudies-literature
Project description:CCP4mg is a molecular-graphics program that is designed to give rapid access to both straightforward and complex static and dynamic representations of macromolecular structures. It has recently been updated with a new interface that provides more sophisticated atom-selection options and a wizard to facilitate the generation of complex scenes. These scenes may contain a mixture of coordinate-derived and abstract graphical objects, including text objects, arbitrary vectors, geometric objects and imported images, which can enhance a picture and eliminate the need for subsequent editing. Scene descriptions can be saved to file and transferred to other molecules. Here, the substantially enhanced version 2 of the program, with a new underlying GUI toolkit, is described. A built-in rendering module produces publication-quality images.
| S-EPMC3069754 | biostudies-literature
Project description:Imaging can be thought of as the most direct of experiments. You see something; you report what you see. If only things were truly this simple. Modern imaging technology has brought about a revolution in the kinds of questions we can approach, but this comes at the price of increasingly complex equipment. Moreover, in an attempt to market competing systems, the microscopes have often been inappropriately described as easy to use and suitable for near-beginners. Insufficient understanding of the experimental manipulations and equipment set-up leads to the introduction of errors during image acquisition. In this feature, I review some of the most common practical pitfalls faced by researchers during image acquisition, and how they can affect the interpretation of the experimental data. This article is targeted neither to the microscopy gurus who push forward the frontiers of imaging technology nor to my imaging specialist colleagues who may wince at the overly simplistic comments and lack of detail. Instead, this is for beginners who gulp with alarm when they hear the word "confocal pinhole" or sigh as they watch their cells fade and die in front of their very eyes time and time again at the microscope. Take heart, beginners, if microscopes were actually so simple then many people (including myself) would suddenly be out of a job!
| S-EPMC2063524 | biostudies-literature
Project description:High-throughput assays for measuring the three-dimensional (3D) configuration of DNA have provided unprecedented insights into the relationship between DNA 3D configuration and function. Data interpretation from assays such as ChIA-PET and Hi-C is challenging because the data is large and cannot be easily rendered using standard genome browsers. An effective Hi-C visualization tool must provide several visualization modes and be capable of viewing the data in conjunction with existing, complementary data. We review five software tools that do not require programming expertise. We summarize their complementary functionalities, and highlight which tool is best equipped for specific tasks.
| S-EPMC5290626 | biostudies-literature
Project description:BackgroundThe diagnostic yields and safety profiles of transbronchial lung biopsy have not been evaluated in inexperienced physicians using the combined modality of radial probe endobronchial ultrasound and a guide sheath (EBUS-GS). This study assessed the utility and safety of EBUS-GS during the learning phase by referring to a database of performed EBUS-GS procedures.MethodsFrom December 2015 to January 2017, all of the consecutive patients who underwent EBUS-GS were registered. During the study period, two physicians with no previous experience performed the procedure. To assess the diagnostic yields, learning curve, and safety profile of EBUS-GS performed by these inexperienced physicians, the first 100 consecutive EBUS-GS procedures were included in the evaluation.ResultsThe overall diagnostic yield of EBUS-GS performed by two physicans in 200 patients with a peripheral lung lesion was 73.0%. Learning curve analyses showed that the diagnostic yields were stable, even when the procedure was performed by beginners. Complications related to EBUS-GS occurred in three patients (1.5%): pneumothorax developed in two patients (1%) and resolved spontaneously without chest tube drainage; another patient (0.5%) developed a pulmonary infection after EBUS-GS. There were no cases of pneumothorax requiring chest tube drainage, severe hemorrhage, respiratory failure, premature termination of the procedure, or procedure-related mortality.ConclusionsEBUS-GS is a safe and stable procedure with an acceptable diagnostic yield, even when performed by physicians with no previous experience.
| S-EPMC6090614 | biostudies-literature
Project description:Cadaveric dissection of temporal bone anatomy is not always possible or feasible in certain educational environments. Volume rendering using CT and/or MRI helps understanding spatial relationships, but they suffer in nonrealistic depictions especially regarding color of anatomical structures. Freely available, nonstained histological data sets and software which are able to render such data sets in realistic color could overcome this limitation and be a very effective teaching tool.With recent availability of specialized public-domain software, volume rendering of true-color, histological data sets is now possible. We present both feasibility as well as step-by-step instructions to allow processing of publicly available data sets (Visible Female Human and Visible Ear) into easily navigable 3-dimensional models using free software.Example renderings are shown to demonstrate the utility of these free methods in virtual exploration of the complex anatomy of the temporal bone. After exploring the data sets, the Visible Ear appears more natural than the Visible Human.We provide directions for an easy-to-use, open-source software in conjunction with freely available histological data sets. This work facilitates self-education of spatial relationships of anatomical structures inside the human temporal bone as well as it allows exploration of surgical approaches prior to cadaveric testing and/or clinical implementation.
| S-EPMC4410986 | biostudies-literature
Project description:Twirling is a technique widely used for converting arbitrary noise channels into Pauli channels in error threshold estimations of quantum error correction codes. It is vitally useful both in real experiments and in classical quantum simulations. Minimising the size of the twirling gate set increases the efficiency of simulations and in experiments it might reduce both the number of runs required and the circuit depth (and hence the error burden). Conventional twirling uses the full set of Pauli gates as the set of twirling gates. This article provides a theoretical background for Pauli twirling and a way to construct a twirling gate set with a number of members comparable to the size of the Pauli basis of the given error channel, which is usually much smaller than the full set of Pauli gates. We also show that twirling is equivalent to stabiliser measurements with discarded measurement results, which enables us to further reduce the size of the twirling gate set.
| S-EPMC6677783 | biostudies-literature
Project description:MotivationHigh-throughput biological research requires simultaneous visualization as well as analysis of genomic data, e.g. read alignments, variant calls and genomic annotations. Traditionally, such integrative analysis required desktop applications operating on locally stored data. Many current terabyte-size datasets generated by large public consortia projects, however, are already only feasibly stored at specialist genome analysis centers. As even small laboratories can afford very large datasets, local storage and analysis are becoming increasingly limiting, and it is likely that most such datasets will soon be stored remotely, e.g. in the cloud. These developments will require web-based tools that enable users to access, analyze and view vast remotely stored data with a level of sophistication and interactivity that approximates desktop applications. As rapidly dropping cost enables researchers to collect data intended to answer questions in very specialized contexts, developers must also provide software libraries that empower users to implement customized data analyses and data views for their particular application. Such specialized, yet lightweight, applications would empower scientists to better answer specific biological questions than possible with general-purpose genome browsers currently available.ResultsUsing recent advances in core web technologies (HTML5), we developed Scribl, a flexible genomic visualization library specifically targeting coordinate-based data such as genomic features, DNA sequence and genetic variants. Scribl simplifies the development of sophisticated web-based graphical tools that approach the dynamism and interactivity of desktop applications.Availability and implementationSoftware is freely available online at http://chmille4.github.com/Scribl/ and is implemented in JavaScript with all modern browsers supported.
| S-EPMC3562066 | biostudies-literature
Project description:BACKGROUND:Virtual implant planning systems integrate (cone beam-) computed tomography data to assess bone quantity and virtual models for the design of the implant-retained prosthesis and drill guides. Five commercially available systems for virtual implant planning were examined regarding the modalities of integration of radiographic data, virtual dental models and the design of drill guides for guided implant surgery. The purpose of this review was to describe the limitations of these available systems regarding the import of imaging data and the design and fabrication of a drill guide. METHODS:The following software systems were examined regarding the import of imaging data and the export of the virtual implant planning for the design and fabrication of a drill guide with the help of two clinical situations requiring dental implant therapy: coDiagnostiX™, DentalWings, Canada (CDX); Simplant Pro™, Dentsply, Sweden (SIM); Smop™, Swissmeda, Switzerland (SMP); NobelClinician™, Nobel Biocare, Switzerland (NC); Implant Studio, 3Shape, Denmark (IST). Assessment criteria included data formats and management as well as the workflow for the design and production of drill guides. RESULTS:All systems have a DICOM-interface ("Digital Imaging and Communication in Medicine") for the import of radiographic data. Imaging artefacts could be reduced but not eliminated by manual data processing. The import of virtual dental models in a universal format (STL: Standard Tesselation Language) was possible with three systems; one system could only be used with a proprietary data format. All systems display three-dimensional surface models or two-dimensional cross-sections with varying orientation for virtual implant planning. Computer aided design and manufacturing (CAD/CAM) of drill guides may be performed by the user with the help of default parameters or solely by the provider of the software and thus without the influence of the clinician. CONCLUSION:Data bases of commonly used implant systems are available in all tested software, however not all systems allow to plan and execute fully guided implant placement. An individual design and in-house manufacturing of the drill guide is only available in some software systems. However, at the time of publication most recent software versions showed flexibility in individual design and in-house manufacturing of drill guides.
| S-EPMC7488021 | biostudies-literature
Project description:Homologous recombination between the maternal and paternal copies of a chromosome is a key mechanism for human inheritance and shapes population genetic properties of our species. However, a similar mechanism can also act between different copies of the same sequence, then called non-allelic homologous recombination (NAHR). This process can result in genomic rearrangements-including deletion, duplication, and inversion-and is underlying many genomic disorders. Despite its importance for genome evolution and disease, there is a lack of computational models to study genomic loci prone to NAHR. In this work, we propose such a computational model, providing a unified framework for both (allelic) homologous recombination and NAHR. Our model represents a set of genomes as a graph, where haplotypes correspond to walks through this graph. We formulate two founder set problems under our recombination model, provide flow-based algorithms for their solution, describe exact methods to characterize the number of recombinations, and demonstrate scalability to problem instances arising in practice.
| S-EPMC10543304 | biostudies-literature